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https://github.com/batmen-lab/miostone

Modeling microbiome-trait associations with taxonomy-adaptive neural networks

https://github.com/batmen-lab/miostone

Science Score: 13.0%

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    CITATION.cff file
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    Found codemeta.json file
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    .zenodo.json file
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    Low similarity (4.8%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Modeling microbiome-trait associations with taxonomy-adaptive neural networks

Basic Info
  • Host: GitHub
  • Owner: batmen-lab
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 13.3 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

MIOSTONE

Source code for MIOSTONE: Modeling microbiome-trait associations with taxonomy-adaptive neural networks

Dataset

Please unzip the data.tar.xz file and put the data directory in the same directory as the src directory.

Example Notebook

An example jupyter notebook is provided in the example directory. Please follow the instructions in the notebook to run MIOSTONE on the example dataset.

Requirements

Required packages are listed in environment.yml. You can create a conda environment with the following command:

bash conda env create -f environment.yml

Owner

  • Name: BATMEN Lab @ UWaterloo
  • Login: batmen-lab
  • Kind: user
  • Company: UWaterloo CS

GitHub Events

Total
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Last Year
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Dependencies

requirements.txt pypi
  • aom =3.7.0=h59595ed_0
  • archspec =0.2.2=pyhd8ed1ab_0
  • asttokens =2.4.1=pyhd8ed1ab_0
  • atk-1.0 =2.38.0=hd4edc92_1
  • backcall =0.2.0=pyhd3eb1b0_0
  • backports =1.1=pyhd3eb1b0_0
  • backports.functools_lru_cache =1.6.5=pyhd8ed1ab_0
  • blas =1.0=mkl
  • blas-devel =3.9.0=12_linux64_mkl
  • boltons =23.0.0=py311h06a4308_0
  • boost-cpp =1.82.0=hdb19cb5_2
  • bottleneck =1.3.7=py311h1f0f07a_1
  • brotli =1.1.0=hd590300_1
  • brotli-bin =1.1.0=hd590300_1
  • brotli-python =1.1.0=py311hb755f60_1
  • bzip2 =1.0.8=h7b6447c_0
  • c-ares =1.21.0=hd590300_0
  • ca-certificates =2023.08.22=h06a4308_0
  • cachecontrol =0.13.1=pyhd8ed1ab_0
  • cached-property =1.5.2=py_0
  • cairo =1.18.0=h3faef2a_0
  • captum =0.6.0=0
  • certifi =2023.7.22=py311h06a4308_0
  • cffi =1.16.0=py311hb3a22ac_0
  • charset-normalizer =3.3.2=pyhd8ed1ab_0
  • colorama =0.4.6=py311h06a4308_0
  • comm =0.1.4=pyhd8ed1ab_0
  • conda =23.10.0=py311h06a4308_0
  • conda-content-trust =0.2.0=py311h06a4308_0
  • conda-libmamba-solver =23.11.0=py311h06a4308_0
  • conda-package-handling =2.2.0=py311h06a4308_0
  • conda-package-streaming =0.9.0=py311h06a4308_0
  • contourpy =1.2.0=py311h9547e67_0
  • cryptography =41.0.5=py311h63ff55d_0
  • cuda =11.7.1=0
  • cuda-cccl =11.7.91=0
  • cuda-command-line-tools =11.7.1=0
  • cuda-compiler =11.7.1=0
  • cuda-cudart =11.7.99=0
  • cuda-cudart-dev =11.7.99=0
  • cuda-cuobjdump =11.7.91=0
  • cuda-cupti =11.7.101=0
  • cuda-cuxxfilt =11.7.91=0
  • cuda-demo-suite =12.3.52=0
  • cuda-documentation =12.3.52=0
  • cuda-driver-dev =11.7.99=0
  • cuda-gdb =12.3.52=0
  • cuda-libraries =11.7.1=0
  • cuda-libraries-dev =11.7.1=0
  • cuda-memcheck =11.8.86=0
  • cuda-nsight =12.3.52=0
  • cuda-nsight-compute =12.3.0=0
  • cuda-nvcc =11.7.99=0
  • cuda-nvdisasm =12.3.52=0
  • cuda-nvml-dev =11.7.91=0
  • cuda-nvprof =12.3.52=0
  • cuda-nvprune =11.7.91=0
  • cuda-nvrtc =11.7.99=0
  • cuda-nvrtc-dev =11.7.99=0
  • cuda-nvtx =11.7.91=0
  • cuda-nvvp =12.3.52=0
  • cuda-runtime =11.7.1=0
  • cuda-sanitizer-api =12.3.52=0
  • cuda-toolkit =11.7.1=0
  • cuda-tools =11.7.1=0
  • cuda-version =11.8=h70ddcb2_2
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  • cudatoolkit =11.8.0=h6a678d5_0
  • cudnn =8.9.2.26=cuda11_0
  • cycler =0.12.1=pyhd8ed1ab_0
  • cyrus-sasl =2.1.28=h52b45da_1
  • cython =3.0.5=py311hb755f60_0
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  • expat =2.5.0=h6a678d5_0
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  • glib =2.78.1=hfc55251_0
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  • intel-openmp =2021.4.0=h06a4308_3561
  • ipykernel =6.26.0=pyhf8b6a83_0
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  • lcms2 =2.15=hfd0df8a_0
  • ld_impl_linux-64 =2.40=h41732ed_0
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  • tomli =2.0.1=py311h06a4308_0
  • torchaudio =2.1.1=py311_cpu
  • torchmetrics =1.2.0=pyhd8ed1ab_0
  • torchtriton =2.1.0=py311
  • torchvision =0.16.1=py311_cpu
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  • urllib3 =1.26.18=py311h06a4308_0
  • wcwidth =0.2.10=pyhd8ed1ab_0
  • wheel =0.41.3=pyhd8ed1ab_0
  • widgetsnbextension =4.0.9=pyhd8ed1ab_0
  • x264 =1
  • x265 =3.5=h924138e_3
  • xorg-fixesproto =5.0=h7f98852_1002
  • xorg-kbproto =1.0.7=h7f98852_1002
  • xorg-libice =1.1.1=hd590300_0
  • xorg-libsm =1.2.4=h7391055_0
  • xorg-libx11 =1.8.7=h8ee46fc_0
  • xorg-libxau =1.0.11=hd590300_0
  • xorg-libxdmcp =1.1.3=h7f98852_0
  • xorg-libxext =1.3.4=h0b41bf4_2
  • xorg-libxfixes =5.0.3=h7f98852_1004
  • xorg-libxrender =0.9.11=hd590300_0
  • xorg-renderproto =0.11.1=h7f98852_1002
  • xorg-xextproto =7.3.0=h0b41bf4_1003
  • xorg-xproto =7.0.31=h27cfd23_1007
  • xz =5.4.2=h5eee18b_0
  • yaml =0.2.5=h7b6447c_0
  • yaml-cpp =0.8.0=h6a678d5_0
  • zeromq =4.3.5=h59595ed_0
  • zipp =3.17.0=pyhd8ed1ab_0
  • zlib =1.2.13=hd590300_5
  • zstandard =0.22.0=py311haa97af0_0
  • zstd =1.5.5=hc292b87_0